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Software Licensed by the Science Library: Features and Tools

The Robin Li and Melissa Ma Science Library has purchased campus-wide site licenses for several products. Access to all of these products is limited to current Stanford students, faculty, and staff.

Platform Overview

An alphabetical list describing each software component is available at the bottom of this page.


Biologics Drug Discovery Suite

All the tools that are important in modeling biologics, antibodies, and proteins. 

A unified entry point for molecular insights and access to integrated solutions for: Structure Prediction, Characterization & Liability Analysis, and Protein Engineering.


Available components: BioLuminate, Desmond, KNIME Extensions, Maestro, OPLS3, PIPER, Prime, Protein Preparation Wizard, SiteMap.


Small-Molecule Drug Discovery Suite

A comprehensive suite to accelerate lead discovery and lead optimization. 


From quantitative structure activity relationships (QSAR) to virtual screening to binding affinity predictions, the comprehensive Small-Molecule Drug Discovery Suite contains all the tools necessary for fragment-, ligand-, and structure-based drug design for lead discovery and optimization. 

Available Components: AutoQSAR, Canvas, ConfGen, Core Hopping, CovDock, Desmond, Epik, Field-Based QSAR, Glide, Induced Fit, Jaguar, KNIME Extensions, LigPrep, MacroModel, Maestro, MOPAC2012, OPLS3, P450 Site of Metabolism Prediction, Phase, PLDB, Prime, PrimeX, Protein Preparation Wizard, QikProp, QM-Polarized Docking, QSite, Shape Screening, and SiteMap.  MOPAC2012 must be installed separately.

Materials Science Suite

A diverse set of tools for computing the structure, reactivity, and properties of chemical systems. 

This innovative new suite provides versatile and powerful tools for the quantum mechanics-based simulation of chemical systems, enabling the analysis and optimization of systems with applications in specialty chemicals and materials science. 

Available Components:  Canvas, Desmond, KNIME Extensions, MacroModel, Maestro, MOPAC2012, MS Combi, MS Jaguar, OPLS3.  MOPAC2012 must be installed separately.


Oak Storage Additional Features

Commercial compound databases tailored to use with Phase

Schrödinger has partnered with Enamine, MilliporeSigma, and MolPort to provide a Phase database of fragments, lead-like, near drug-like, and drug-like compounds available from Enamine's "Stock Screening Compounds Collection", MilliporeSigma's "Aldrich Market Select", and MolPort's "Screening Compound Database" respectively.  The MolPort and Sigma DBs are about 800 GB and the Enamine one about 340 GB.  The databases can be updated quarterly to ensure compound availability and enable out-of-the-box virtual screening. Top-ranked compounds from a virtual screen can be easily purchased by ID directly from the compound vendors.  Learn more about Phase software.

The Stanford Libraries have purchased MilliporeSigma's "Aldrich Market Select" database which we are updating annually and storing on the Oak Storage Server.   In order to use the Aldrich Market Select database with Schrödinger Phase software, you must copy the database into your Sherlock 3 space where Schrodinger is stored.

Instructions for copying Aldrich Market Select to Sherlock 3.0

Please note: Users need to be added to both the sw_schrodinger group on Sherlock and the Stanford workgroup oak:p-sul-schrodinger.  

Copying Instructions:

Access the CACDB (in read-only) anywhere on Sherlock at the following path:


It's just ready to go from there.

But if you want to copy the CACDB to your own storage space, you can use Globus in the following way:

1. Go to and select "Stanford University" then authenticate using your regular SUNet ID credentials using Duo.

2. A "Transfer Files" page will open, with two sides representing the transfer's source and destination.

2.a. On the left side, click on the Endpoint text field and select "SRCC Oak". As the Path, please use the full path to the SUL Schrodinger directory:


2.b. On the right side, click on the Endpoint text field and select "SRCC Sherlock". As the Path, a user can specify where he/she wants the CACDB directory to be copied on Sherlock. By default, the Sherlock Globus endpoint will show the $SCRATCH space (large temporary storage space on Sherlock that is purged after 6 months).

3. Please make sure that only the option "verify file integrity after transfer" is checked at the bottom. I don't recommend to select any other option.

4. When both left and right sides are configured, select the CACDB directory on the left side (Oak) and click on the right arrow to start the transfer of the full CACDB directory to Sherlock.  A user can now close the window and an email will be sent when the transfer has completed (it might take a few hours).

A-Z Component Features

A-Z description of the software

An alphabetical list of the software we have licensed plus the product suite name(s) they are part of is below.



Product Suites

AutoQSAR - Automated creation and application of predictive QSAR models following best practices.   AutoQSAR automates the creation of high-quality, predictive QSAR models and makes their application trivially simple.

Small-Molecule Drug Discovery

BioLuminate - Providing a comprehensive modeling solution for biologics.  BioLuminate is a brand-new, intuitive user interface that is specifically designed for examining biologics and protein systems with seamless access to superior scientific modeling algorithms.  



ConfGen - Accurate and efficient bioactive conformational searching.  Reproducing bioactive ligand geometries in minimally sized conformer sets, accurate results from high-performance ConfGen calculations save time and effort in downstream applications.

Small-Molecule Drug Discovery

Core Hopping - Comprehensive ligand- and receptor-based scaffold exploration for lead optimization.  In addition to more conventional ligand-based methods, Core Hopping offers receptor-based scaffold hopping, exploiting information about the active site and known binding poses to guide the search for novel cores.

Small-Molecule Drug Discovery

Desmond - High-performance molecular dynamics simulations.  Desmond's combined speed and accuracy make possible long time scale molecular dynamics simulations, allowing users to examine events of great biological and pharmaceutical importance. Seamlessly integrated with Maestro, Desmond provides comprehensive setup, simulation, and analysis tools.

Biologics, Small-Molecule Drug Discovery, and Materials Science

Epik - Rapid and robust pKa predictions. Combining the proven reliability of Hammett and Taft methods with powerful tautomerization tools, Epik is the program of choice for accurate enumeration of ligand protonation states in biological conditions.

Small-Molecule Drug Discovery

Field-Based QSAR - Discover and optimize new lead compounds using quantitative predictions of binding-site chemistry.  Field-Based QSAR opens up new possibilities in ligand-based drug discovery projects. Supplied with an aligned training set of active and inactive compounds, Field-Based QSAR predicts drug activity on the basis of either force fields or Gaussian fields that describe ligand chemistry.

Small-Molecule Drug Discovery

Glide - A complete solution for ligand-receptor docking. Glide offers the full spectrum of speed and accuracy from high-throughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at every level.

Small-Molecule Drug Discovery

Glide XP Visualizer – a tool for viewing Glide descriptors.  Glide offers the full range of speed vs. accuracy options, from the HTVS (high-throughput virtual screening) mode for efficiently enriching million compound libraries, to the SP (standard precision) mode for reliably docking tens to hundreds of thousands of ligand with high accuracy, to the XP (extra precision) mode where further elimination of false positives is accomplished by more extensive sampling and advanced scoring, resulting in even higher enrichment. The size of the dataset that needs to be studied at each level of accuracy is approximately an order of magnitude smaller than that of the previous, faster step. XP provides the most accurately docked poses and the highest level of enrichment.  The XP Visualizer is in Glide.

Small-Molecule Drug Discovery


Induced Fit - A novel method for fast and accurate prediction of ligand induced conformational changes in receptor active sites. The active site geometry of a protein complex depends heavily upon conformational changes induced by the bound ligand. However, resolving the crystallographic structure of a protein-ligand complex requires a substantial investment of time, and is frequently infeasible or impossible. Schrödinger's Induced Fit protocol solves this problem by using Glide and Prime to exhaustively consider possible binding modes and the associated conformational changes within receptor active sites.

Small-Molecule Drug Discovery

Jaguar - Rapid ab initio electronic structure package. Jaguar is a high-performance ab initio package for both gas and solution phase simulations, with particular strength in treating metal containing systems, making it the most practical quantum mechanical tool for solving real-world problems.

Small-Molecule Drug Discovery, and Materials Science
 Jaguar pKa

Jaguar pKa: A KNIME Workflow to evaluate the pKa of specified atoms using Jaguar.

Small-Molecule Drug Discovery

KNIME Extensions  - A modular, highly configurable framework for easy workflow automation and data analysis.  Using the popular open-source KNIME interface, researchers can easily assemble individual "nodes" into a complete workflow — from structure preparation and selection to a validated predictive model. Expediting a wide variety of common tasks, Schrödinger KNIME Extensions are an indispensable tool for modeling and cheminformatics.

Biologics, Small-Molecule Drug Discovery, and Materials Science

LigPrep - Versatile generation of accurate 3D molecular models.  LigPrep goes far beyond simple 2D to 3D structure conversions by including tautomeric, stereochemical, and ionization variations, as well as energy minimization and flexible filters to generate fully customized ligand libraries for further computational analyses.

Small-Molecule Drug Discovery

MacroModel - Versatile, full-featured program for molecular modeling.  MacroModel combines leading force fields, accurate effective solvation models, and advanced conformational searching methods to provide the most complete molecular modeling package suitable for a wide array of research.

Small-Molecule Drug Discovery, and Materials Science

Maestro 11 - The completely reimagined all-purpose molecular modeling environment. Maestro 11 is the completely redesigned interface for all Schrödinger software. Significantly enhanced usability built on Maestro’s long-standing impressive visualization and analysis tools makes Maestro 11 a versatile modeling environment for all researchers.

Biologics, Small-Molecule Drug Discovery, and Materials Science

Membrane Permeability - Physics-based, accurate predictions of passive membrane permeability. The Prime physics-based membrane predictor combines conformational sampling with Schrödinger’s advanced force field and solvent models within a physics-based framework to produce more accurate predictions of passive membrane permeability.

Biologics, and Small-Molecule Drug Discovery

MOPAC2012 - Fast, accurate quantum chemistry for large structures and condensed phase.   Schrödinger provides access to MOPAC2012 for basic semiempirical NDDO (neglect of diatomic differential overlap) capabilities. With this tool you can calculate heats of formation, optimized geometries, force constants, and a selection of properties as indicated below. This semiempirical NDDO program can be run from Maestro or from the command line.

Produced by Stewart Computational Chemistry and free to academic users, MOPAC2012 has been integrated to work with Schrödinger software but only MOPAC2016 is available for downloading. Instructions for modifying 2016 to 2012: Copy MOPAC2016.exe and rename the copy MOPAC2012.exe.   Copy "password for MOPAC2016" and rename the copy "password for MOPAC2012" You should then have two MOPAC executables and two passwords.  Then try running the Schrodinger software.

Small-Molecule Drug Discovery, and Materials Science

MS Maestro – A specialized interface to enable efficient and systematic exploration of chemical design space for key technology applications including optoelectronics and reactive systems. 

Materials Science

OPLS3e - A revolutionary advance in modern force fields. OPLS3 is the culmination of a significant, large-scale effort to create the most accurate force field with the most comprehensive coverage of chemical space. OPLS3 with a new version of the force field (OPLS3e, “e” for extended) that includes significant advances in accuracy in modeling small molecules and protein-ligand binding.

Biologics, Small-Molecule Drug Discovery, and Materials Science
 Cytochrome P450 Oxidase

P450 Site of Metabolism (SOM) Prediction - A tool is used for identifying likely sites of metabolism based on Hammet and Taft- type rules and 3D spatial information in several P450 isoforms.  For a given atom of a molecule to be a significant site of metabolism by a P450 enzyme, it must have some degree of reactivity in the absence of the enzyme and also be accessible to the reactive heme iron center. To address both of these requirements, the P450 Site of Metabolism workflow combines induced-fit docking (IFD) for the determination of accessibility to the reactive center with a rule-based approach to intrinsic reactivity.  Note: password required to link in this description.

Small-Molecule Drug Discovery

Phase - An easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design.  Phase is a complete, user-friendly pharmacophore modeling solution designed to maximize performance in virtual screening and lead optimization. Fast, accurate, and easy-to-use, Phase includes a novel, scientifically validated common pharmacophore perception algorithm.  MilliporeSigma's "Aldrich Market Select" that contains commercially available compounds to use with Phase is also available to Stanford users.  Please see: Oak Storage Server instructions to get a copy of Aldrich Market Select database

Biologics, and Small-Molecule Drug Discovery

PIPER - A state of the art protein-protein docking program. PIPER is a state-of-the-art protein-protein docking program based on a multi-staged approach and advanced numerical methods that reliably generates accurate structures of protein-protein complexes.


Prime - A powerful and innovative package for accurate protein structure predictions. Prime is a fully-integrated protein structure prediction program. It provides an easy-to-use interface that takes a novice user intuitively from sequence to alignment to refined structure. Prime also provides expert users complete control over calculational settings to maximize accuracy of predictions. Prime is a powerful and complete tool for generating accurate receptor models for structure-based drug design.

Biologics, and Small-Molecule Drug Discovery

PrimeX - A comprehensive package for accurate protein crystal structure refinement.  PrimeX uses state-of-the-art technologies to refine protein crystal structures for computational drug discovery.

Small-Molecule Drug Discovery

Protein Preparation Wizard - An easy-to-use tool for correcting common structural problems and creating reliable, all-atom protein models. Successful structure-based modeling projects demand not only accurate software, but accurate starting structures as well. Left untreated, common problems with experimentally-derived structures can lead to wasted time and resources. Schrödinger’s Protein Preparation Wizard is designed to help researchers ensure structural correctness at the outset of a project, equipping them with a high-confidence structure ideal for use with a wide variety of modeling applications.

Biologics, and Small-Molecule Drug Discovery

PyMOL - Stunning high-performance molecular graphics for communicating structural results.  Tens of thousands of scientists worldwide choose PyMOL to view, share, and analyze their molecular data. In addition to being lightweight and fast, PyMOL can create images of peerless visualization quality, while offering the flexibility of Python-based development and scalability.  AxPyMOL - plugin for Windows PowerPoint that enables presentation of 3-D molecular data without having to "tab out" of PowerPoint slides.   Stanford's site license includes PyMOL and AxPyMOL.


QikProp - Rapid ADME predictions of drug candidates. QikProp efficiently evaluates pharmaceutically relevant properties for over half a million compounds per hour, making it an indispensable lead generation and lead optimization tool.

Small-Molecule Drug Discovery

QM Polarized Ligand Docking - A novel research solution that combines the power of Glide with the accuracy of QSite.  Accurate treatment of electrostatic charges is crucial to the success of any docking algorithm. Although contemporary force fields are capable of modeling partial atomic charges on ligands with reasonable accuracy, they are generally incapable of considering charge polarization induced by the protein environment. The greater the role charge polarization plays in determining a ligand's bound conformation, the more difficult it will be for MM docking algorithms to perceive the correct binding mode. For research applications that demand the highest level of docking accuracy, Schrödinger introduces QM-Polarized Ligand Docking (QPLD), which uses ab inito charge calculations to overcome this limitation.

Small-Molecule Drug Discovery

QSite - A high-performance QM/MM program. QSite applies quantum mechanics to the reactive center of a protein active site and molecular mechanics to the rest of the system. Its accuracy allows detailed understanding of reactions involving proteins, making it a powerful tool for lead optimization.

Small-Molecule Drug Discovery

Schrödinger API - interface that allows python code to be used with our software.  It is accessed using the unlimited MMLIBS token.

Access API module and documentation

Shape Screening - A fast and efficient tool for shape-based superposition and similarity searching. Shape Screening is capable of screening large databases of compounds to identify new leads with similar shape and electrostatic properties to a lead query molecule.

Small-Molecule Drug Discovery

SiteMap - Fast, accurate, and practical binding site identification. Combining a novel algorithm for rapid binding site identification and evaluation with easy-to-use property visualization tools, SiteMap provides researchers with an efficient means to find and better exploit the characteristics of ligand binding sites.